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    NCBP1 nuclear cap binding protein subunit 1 [ Homo sapiens (human) ]

    Gene ID: 4686, updated on 9-Dec-2024

    Summary

    Official Symbol
    NCBP1provided by HGNC
    Official Full Name
    nuclear cap binding protein subunit 1provided by HGNC
    Primary source
    HGNC:HGNC:7658
    See related
    Ensembl:ENSG00000136937 MIM:600469; AllianceGenome:HGNC:7658
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NCBP; Sto1; CBP80
    Summary
    The product of this gene is a component of the nuclear cap-binding protein complex (CBC), which binds to the monomethylated 5' cap of nascent pre-mRNA in the nucleoplasm. The encoded protein promotes high-affinity mRNA-cap binding and associates with the CTD of RNA polymerase II. The CBC promotes pre-mRNA splicing, 3'-end processing, RNA nuclear export, and nonsense-mediated mRNA decay. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 9.3), lymph node (RPKM 7.9) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See NCBP1 in Genome Data Viewer
    Location:
    9q22.33
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (97633821..97673748)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (109805762..109845689)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (100396103..100436030)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100278102-100278602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28666 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100293128-100293286 Neighboring gene tropomodulin 1 Neighboring gene Sharpr-MPRA regulatory region 7780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100318031-100318532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100319241-100319742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28668 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100335093-100335332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28671 Neighboring gene Sharpr-MPRA regulatory region 9871 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:100396128-100396963 Neighboring gene thiosulfate sulfurtransferase like domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20102 Neighboring gene XPA, DNA damage recognition and repair factor Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:100465986-100467185 Neighboring gene keratin 18 pseudogene 13 Neighboring gene papillary thyroid carcinoma susceptibility candidate 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28678 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:100520047-100521246 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:100534165-100534666 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:100534667-100535166 Neighboring gene VISTA enhancer hs1595 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20103 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:100571176-100572375 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100589760-100589981 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100613975-100614476 Neighboring gene forkhead box E1

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    The FOXE1 locus is a major genetic determinant for radiation-related thyroid carcinoma in Chernobyl.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC2087

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA 7-methylguanosine cap binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables RNA binding HDA PubMed 
    enables RNA cap binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables molecular adaptor activity EXP
    Inferred from Experiment
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in 7-methylguanosine mRNA capping IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in RNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in RNA splicing TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in alternative mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in cap-dependent translational initiation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in defense response to virus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in histone mRNA metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mRNA 3'-end processing NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in mRNA export from nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in mRNA export from nucleus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mRNA export from nucleus IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    involved_in mRNA metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in mRNA transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in mRNA transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in miRNA-mediated post-transcriptional gene silencing NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of RNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of mRNA 3'-end processing IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription elongation by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in primary miRNA processing NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of mRNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of translational initiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulatory ncRNA-mediated post-transcriptional gene silencing NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in snRNA export from nucleus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in snRNA export from nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in spliceosomal complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of RNA cap binding complex IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    part_of RNA cap binding complex TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
     
    part_of nuclear cap binding complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of nuclear cap binding complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of nuclear cap binding complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    nuclear cap-binding protein subunit 1
    Names
    80 kDa nuclear cap-binding protein
    NCBP 80 kDa subunit
    nuclear cap binding protein subunit 1, 80kDa

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001351504.2NP_001338433.1  nuclear cap-binding protein subunit 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL445531, BC001450, CA418527, DA885233
      Conserved Domains (3) summary
      smart00543
      Location:9173
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      pfam09088
      Location:284403
      MIF4G_like; MIF4G like
      pfam09090
      Location:418693
      MIF4G_like_2; MIF4G like
    2. NM_001351505.2NP_001338434.1  nuclear cap-binding protein subunit 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL445531, BC001450, CA418527, CN266899
      Conserved Domains (2) summary
      pfam09088
      Location:161280
      MIF4G_like; MIF4G like
      pfam09090
      Location:295570
      MIF4G_like_2; MIF4G like
    3. NM_001351506.2NP_001338435.1  nuclear cap-binding protein subunit 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL445531, BC001450, CA418527, CN266899, DA885233
      Conserved Domains (2) summary
      pfam09088
      Location:161280
      MIF4G_like; MIF4G like
      pfam09090
      Location:295570
      MIF4G_like_2; MIF4G like
    4. NM_001351507.2NP_001338436.1  nuclear cap-binding protein subunit 1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL445531, BC001450, CA418527
      Conserved Domains (2) summary
      pfam09088
      Location:2100
      MIF4G_like; MIF4G like
      pfam09090
      Location:115389
      MIF4G_like_2; MIF4G like
    5. NM_002486.5NP_002477.1  nuclear cap-binding protein subunit 1 isoform 1

      See identical proteins and their annotated locations for NP_002477.1

      Status: REVIEWED

      Source sequence(s)
      AL445531, BC001450, CA418527
      Consensus CDS
      CCDS6728.1
      UniProtKB/Swiss-Prot
      B2R718, Q09161, Q59G76, Q5T1V0, Q5T7X2
      Related
      ENSP00000364289.3, ENST00000375147.8
      Conserved Domains (3) summary
      smart00543
      Location:28240
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      pfam09088
      Location:351470
      MIF4G_like; MIF4G like
      pfam09090
      Location:485760
      MIF4G_like_2; MIF4G like

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      97633821..97673748
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      109805762..109845689
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)